Shea et. al. Differential methylation plots (DMRs)

Annotation track of mm10

Functions

To plot heatmap of regions

plot_heatmap_regions <- function(dmrs, bs, cutoff = 0.05, cutoffCol = "pval",
                                 aggregateRegions = T, aggrFun = "mean", pCols,
                                 minOverlap = 1000, rrbs = NULL) {
  beta <- get_matrix(bs = bs, type = "beta")
  reg <- dmrs[data.frame(dmrs[, cutoffCol])[, cutoffCol] <= cutoff, ]

  overlap <- suppressWarnings(findOverlaps(subject = reg, query = GRanges(beta), type = "within"))
  res1 <- data.frame(reg[overlap@to, ], stringsAsFactors = F)
  res2 <- data.frame(GRanges(beta)[overlap@from], stringsAsFactors = F)
  res <- cbind(res1, res2)
  res <- res[!duplicated(res), c(1:11, 20:ncol(res))]
  res$ID <- paste(res[, 1], res[, 2], res[, 3], sep = "-")

  # overlap.M <- suppressWarnings(findOverlaps(subject = reg, query = GRanges(all$M), type = "within"))
  # res1.M <- data.frame(reg[overlap.M@to, ], stringsAsFactors = F)
  # res2.M <- data.frame(GRanges(all$M)[overlap.M@from], stringsAsFactors = F)
  # res.M <- cbind(res1.M, res2.M)
  # res.M <- res.M[!duplicated(res.M), c(1:11, 20:ncol(res.M))]
  # res.M$ID <- paste(res.M[, 1], res.M[, 2], res.M[, 3], sep = "-")
  #
  # overlap.Cov <- suppressWarnings(findOverlaps(subject = reg, query = GRanges(all$Cov), type = "within"))
  # res1.Cov <- data.frame(reg[overlap.Cov@to, ], stringsAsFactors = F)
  # res2.Cov <- data.frame(GRanges(all$Cov)[overlap.Cov@from], stringsAsFactors = F)
  # res.Cov <- cbind(res1.Cov, res2.Cov)
  # res.Cov <- res.Cov[!duplicated(res.Cov), c(1:11, 20:ncol(res.Cov))]
  # res.Cov$ID <- paste(res.Cov[, 1], res.Cov[, 2], res.Cov[, 3], sep = "-")

  beta <- res

  # if (aggregateRegions) {
  #   cov <- plag(x = res.Cov[, 12:(ncol(res.Cov) - 1)], by = res.Cov$ID, agFun = median)
  #   m <- plag(x = res.M[, 12:(ncol(res.M) - 1)], by = res.M$ID, agFun = median)
  #   b <- m / cov
  #   r <- res.Cov[, 1:11][!duplicated(res.Cov[, 1:11]), ]
  #   rownames(r) <- paste(r[, 1], r[, 2], r[, 3], sep = "-")
  #   beta <- data.frame(r, b)
  # } else {
  #   cov <- res.Cov[, 12:(ncol(res.Cov) - 1)]
  #   m <- res.M[, 12:(ncol(res.M) - 1)]
  #   b <- m / cov
  #   r <- res.Cov[, 1:11]
  #   beta <- data.frame(r, b)
  # }

  beta <- na.replace(beta, 0)
  beta <- beta[order(beta$pval), ]

  beta.a <- NULL

  if (aggregateRegions) {
    b <- plag(x = beta[, 12:(ncol(beta) - 1)], by = beta$ID, agFun = aggrFun)
    r <- beta[, 1:11][!duplicated(beta[, 1:11]), ]
    rownames(r) <- paste(r[, 1], r[, 2], r[, 3], sep = "-")
    beta.a <- data.frame(r, b)
  } else {
    beta.a <- beta
  }

  beta <- beta.a

  anno.row <- NULL
  anno.col <- NULL
  mat.plot <- NULL
  main <- NULL
  showRownames <- NULL

  if (dim(data.frame(rrbs))[1] > 0) {
    overlap <- suppressWarnings(findOverlaps(subject = GRanges(beta), query = rrbs, minoverlap = minOverlap))
    r1 <- data.frame(GRanges(beta)[overlap@to, ], stringsAsFactors = F)
    r2 <- data.frame(rrbs[overlap@from], stringsAsFactors = F)
    r <- cbind(r1, r2)

    if (dim(data.frame(r))[1] > 0) {
      r$ID <- paste0(as.character(r$seqnames), "-", r$start, "-", r$end, "(", r$geneNames, ")")
      r <- r[!duplicated(r$ID), ]
      rownames(r) <- r$ID
      r <- r[, -ncol(r)]

      anno.row <- data.frame(r[, c(4, 8:11)])
      anno.col <- data.frame(pData(bs)[, pCols], stringsAsFactors = F)

      s <- colnames(data.frame(rrbs))[grep("methRatio", colnames(data.frame(rrbs)))]
      df <- data.frame(ID = s, Age = "", Group = "RRBS")
      rownames(df) <- df$ID
      anno.col <- rbind(anno.col, df[, -1])

      g1 <- unique(anno.col$Group)[1]
      g2 <- unique(anno.col$Group)[2]
      g3 <- unique(anno.col$Group)[3]

      mat <- r
      mat1 <- mat[, rownames(anno.col)[anno.col$Group == g1]]
      mat2 <- mat[, rownames(anno.col)[anno.col$Group == g2]]
      mat3 <- mat[, rownames(anno.col)[anno.col$Group == g3]]
      mat.plot <- data.frame(mat1, mat2, mat3)

      main <- "DMRs beta values (aggregated) + RRBS"
      showRownames <- TRUE
    } else {
      anno.row <- beta[, c(4, 8:11)]
      anno.col <- data.frame(pData(bs)[, pCols], stringsAsFactors = F)

      g1 <- unique(anno.col$Group)[1]
      g2 <- unique(anno.col$Group)[2]

      mat <- beta[, 12:ncol(beta)]
      mat1 <- mat[, rownames(anno.col)[anno.col$Group == g1]]
      mat2 <- mat[, rownames(anno.col)[anno.col$Group == g2]]
      mat.plot <- data.frame(mat1, mat2)

      if (aggregateRegions) {
        main <- "DMRs beta values (aggregated)"
      } else {
        main <- "DMRs beta values (not aggregated)"
      }

      showRownames <- FALSE
    }
  } else {
    anno.row <- beta[, c(4, 8:11)]
    anno.col <- data.frame(pData(bs)[, pCols], stringsAsFactors = F)

    g1 <- unique(anno.col$Group)[1]
    g2 <- unique(anno.col$Group)[2]

    mat <- beta[, 12:ncol(beta)]
    mat1 <- mat[, rownames(anno.col)[anno.col$Group == g1]]
    mat2 <- mat[, rownames(anno.col)[anno.col$Group == g2]]
    mat.plot <- data.frame(mat1, mat2)

    if (aggregateRegions) {
      main <- "DMRs beta values (aggregated)"
    } else {
      main <- "DMRs beta values (not aggregated)"
    }

    showRownames <- FALSE
  }

  pheatmap(
    mat = mat.plot, color = viridis(n = 100), cluster_cols = F,
    show_rownames = showRownames, show_colnames = F,
    cluster_rows = F, annotation_row = anno.row,
    annotation_col = anno.col, border_color = NA,
    main = main
  )
}

Histograms of p-values

HighFat vs CTRL

LowProtein vs CTRL

LowProtein vs HighFat

DMR tables

HighFat vs CTRL

LowProtein vs CTRL

LowProtein vs HighFat

DMR plots

HighFat vs CTRL

Region 1

Region 2

Region 3

Region 4

Region 5

LowProtein vs CTRL

Region 1

Region 2

Region 3

Region 4

Region 5

LowProtein vs HighFat

Region 1

Region 2

Region 3

Region 4

Region 5

Heatmap of Beta values

SessionInfo

## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.3 (2019-03-11)
##  os       Ubuntu 16.04.6 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2019-04-30                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package                            * version   date       lib
##  acepack                              1.4.1     2016-10-29 [1]
##  annotate                             1.60.1    2019-03-07 [1]
##  AnnotationDbi                      * 1.44.0    2018-10-30 [1]
##  AnnotationHub                        2.14.5    2019-03-14 [1]
##  annotatr                             1.8.0     2018-10-30 [1]
##  assertthat                           0.2.1     2019-03-21 [1]
##  backports                            1.1.4     2019-04-10 [1]
##  base64enc                            0.1-3     2015-07-28 [1]
##  bibtex                               0.4.2     2017-06-30 [1]
##  Biobase                            * 2.42.0    2018-10-30 [1]
##  BiocGenerics                       * 0.28.0    2018-10-30 [1]
##  BiocManager                          1.30.4    2018-11-13 [1]
##  BiocParallel                       * 1.16.6    2019-02-10 [1]
##  biomaRt                              2.38.0    2018-10-30 [1]
##  Biostrings                           2.50.2    2019-01-03 [1]
##  bit                                  1.1-14    2018-05-29 [1]
##  bit64                                0.9-7     2017-05-08 [1]
##  bitops                               1.0-6     2013-08-17 [1]
##  blob                                 1.1.1     2018-03-25 [1]
##  bookdown                             0.9       2018-12-21 [1]
##  BSgenome                             1.50.0    2018-10-30 [1]
##  bsseq                              * 1.18.0    2018-10-30 [1]
##  bumphunter                           1.24.5    2018-12-01 [1]
##  callr                                3.2.0     2019-03-15 [1]
##  cellranger                           1.1.0     2016-07-27 [1]
##  checkmate                            1.9.1     2019-01-15 [1]
##  cli                                  1.1.0     2019-03-19 [1]
##  cluster                              2.0.8     2019-04-05 [1]
##  codetools                            0.2-16    2018-12-24 [1]
##  colorspace                           1.4-1     2019-03-18 [1]
##  crayon                               1.3.4     2017-09-16 [1]
##  crosstalk                            1.0.0     2016-12-21 [1]
##  curl                                 3.3       2019-01-10 [1]
##  data.table                         * 1.12.2    2019-04-07 [1]
##  DBI                                  1.0.0     2018-05-02 [1]
##  DelayedArray                       * 0.8.0     2018-10-30 [1]
##  DelayedMatrixStats                   1.4.0     2018-10-30 [1]
##  desc                                 1.2.0     2018-05-01 [1]
##  DESeq2                               1.22.2    2019-01-04 [1]
##  devtools                             2.0.2     2019-04-08 [1]
##  digest                               0.6.18    2018-10-10 [1]
##  dmrseq                             * 1.2.5     2019-03-25 [1]
##  doRNG                                1.7.1     2018-06-22 [1]
##  dplyr                                0.8.0.1   2019-02-15 [1]
##  DT                                   0.5       2018-11-05 [1]
##  edgeR                                3.24.3    2019-01-02 [1]
##  evaluate                             0.13      2019-02-12 [1]
##  foreach                              1.4.4     2017-12-12 [1]
##  forecast                             8.7       2019-04-29 [1]
##  foreign                              0.8-71    2018-07-20 [1]
##  Formula                              1.2-3     2018-05-03 [1]
##  fracdiff                             1.4-2     2012-12-02 [1]
##  fs                                   1.2.7     2019-03-19 [1]
##  genefilter                           1.64.0    2018-10-30 [1]
##  geneplotter                          1.60.0    2018-10-30 [1]
##  GenomeInfoDb                       * 1.18.2    2019-02-12 [1]
##  GenomeInfoDbData                     1.2.0     2019-01-17 [1]
##  GenomicAlignments                    1.18.1    2019-01-04 [1]
##  GenomicFeatures                    * 1.34.8    2019-04-10 [1]
##  GenomicRanges                      * 1.34.0    2018-10-30 [1]
##  ggplot2                            * 3.1.1     2019-04-07 [1]
##  glue                                 1.3.1     2019-03-12 [1]
##  gridExtra                            2.3       2017-09-09 [1]
##  gtable                               0.3.0     2019-03-25 [1]
##  gtools                               3.8.1     2018-06-26 [1]
##  HDF5Array                            1.10.1    2018-12-05 [1]
##  highr                                0.8       2019-03-20 [1]
##  Hmisc                                4.2-0     2019-01-26 [1]
##  hms                                  0.4.2     2018-03-10 [1]
##  htmlTable                            1.13.1    2019-01-07 [1]
##  htmltools                            0.3.6     2017-04-28 [1]
##  htmlwidgets                          1.3       2018-09-30 [1]
##  httpuv                               1.5.1     2019-04-05 [1]
##  httr                                 1.4.0     2018-12-11 [1]
##  imputeTS                           * 2.7       2018-06-20 [1]
##  interactiveDisplayBase               1.20.0    2018-10-30 [1]
##  IRanges                            * 2.16.0    2018-10-30 [1]
##  iterators                            1.0.10    2018-07-13 [1]
##  jsonlite                             1.6       2018-12-07 [1]
##  knitr                                1.22      2019-03-08 [1]
##  labeling                             0.3       2014-08-23 [1]
##  later                                0.8.0     2019-02-11 [1]
##  lattice                              0.20-38   2018-11-04 [1]
##  latticeExtra                         0.6-28    2016-02-09 [1]
##  lazyeval                             0.2.2     2019-03-15 [1]
##  limma                                3.38.3    2018-12-02 [1]
##  lmtest                               0.9-36    2018-04-04 [1]
##  locfit                               1.5-9.1   2013-04-20 [1]
##  magrittr                             1.5       2014-11-22 [1]
##  Matrix                               1.2-17    2019-03-22 [1]
##  matrixStats                        * 0.54.0    2018-07-23 [1]
##  memoise                              1.1.0     2017-04-21 [1]
##  mime                                 0.6       2018-10-05 [1]
##  miniUI                               0.1.1.1   2018-05-18 [1]
##  munsell                              0.5.0     2018-06-12 [1]
##  nlme                                 3.1-139   2019-04-09 [1]
##  nnet                                 7.3-12    2016-02-02 [1]
##  org.Mm.eg.db                       * 3.7.0     2019-01-17 [1]
##  outliers                             0.14      2011-01-24 [1]
##  permute                              0.9-5     2019-03-12 [1]
##  pheatmap                           * 1.0.12    2019-01-04 [1]
##  pillar                               1.3.1     2018-12-15 [1]
##  pkgbuild                             1.0.3     2019-03-20 [1]
##  pkgconfig                            2.0.2     2018-08-16 [1]
##  pkgload                              1.0.2     2018-10-29 [1]
##  pkgmaker                             0.27      2018-05-25 [1]
##  plgINS                             * 0.1.5     2019-04-23 [1]
##  plyr                                 1.8.4     2016-06-08 [1]
##  prettyunits                          1.0.2     2015-07-13 [1]
##  processx                             3.3.0     2019-03-10 [1]
##  progress                             1.2.0     2018-06-14 [1]
##  promises                             1.0.1     2018-04-13 [1]
##  ps                                   1.3.0     2018-12-21 [1]
##  purrr                                0.3.2     2019-03-15 [1]
##  quadprog                             1.5-5     2013-04-17 [1]
##  quantmod                             0.4-14    2019-03-24 [1]
##  questionr                            0.7.0     2018-11-26 [1]
##  R.methodsS3                          1.7.1     2016-02-16 [1]
##  R.oo                                 1.22.0    2018-04-22 [1]
##  R.utils                              2.8.0     2019-02-14 [1]
##  R6                                   2.4.0     2019-02-14 [1]
##  RColorBrewer                         1.1-2     2014-12-07 [1]
##  Rcpp                                 1.0.1     2019-03-17 [1]
##  RCurl                                1.95-4.12 2019-03-04 [1]
##  readr                                1.3.1     2018-12-21 [1]
##  readxl                             * 1.3.1     2019-03-13 [1]
##  regioneR                             1.14.0    2018-10-30 [1]
##  registry                             0.5-1     2019-03-05 [1]
##  remotes                              2.0.4     2019-04-10 [1]
##  reshape2                             1.4.3     2017-12-11 [1]
##  rhdf5                                2.26.2    2019-01-02 [1]
##  Rhdf5lib                             1.4.3     2019-03-25 [1]
##  rlang                                0.3.4     2019-04-07 [1]
##  rmarkdown                            1.12      2019-03-14 [1]
##  rmdformats                           0.3.5     2019-02-19 [1]
##  rngtools                             1.3.1     2018-05-15 [1]
##  rpart                                4.1-15    2019-04-12 [1]
##  rprojroot                            1.3-2     2018-01-03 [1]
##  Rsamtools                            1.34.1    2019-01-31 [1]
##  RSQLite                              2.1.1     2018-05-06 [1]
##  rstudioapi                           0.10      2019-03-19 [1]
##  rtracklayer                        * 1.42.2    2019-03-01 [1]
##  S4Vectors                          * 0.20.1    2018-11-09 [1]
##  scales                               1.0.0     2018-08-09 [1]
##  sessioninfo                          1.1.1     2018-11-05 [1]
##  shiny                                1.3.2     2019-04-22 [1]
##  stinepack                            1.4       2018-07-30 [1]
##  stringi                              1.4.3     2019-03-12 [1]
##  stringr                              1.4.0     2019-02-10 [1]
##  SummarizedExperiment               * 1.12.0    2018-10-30 [1]
##  survival                             2.44-1.1  2019-04-01 [1]
##  testthat                             2.1.1     2019-04-23 [1]
##  tibble                               2.1.1     2019-03-16 [1]
##  tidyselect                           0.2.5     2018-10-11 [1]
##  timeDate                             3043.102  2018-02-21 [1]
##  tseries                              0.10-46   2018-11-19 [1]
##  TTR                                  0.23-4    2018-09-20 [1]
##  TxDb.Mmusculus.UCSC.mm10.knownGene * 3.4.4     2019-01-17 [1]
##  urca                                 1.3-0     2016-09-06 [1]
##  usethis                              1.5.0     2019-04-07 [1]
##  viridis                            * 0.5.1     2018-03-29 [1]
##  viridisLite                        * 0.3.0     2018-02-01 [1]
##  withr                                2.1.2     2018-03-15 [1]
##  xfun                                 0.6       2019-04-02 [1]
##  XML                                  3.98-1.19 2019-03-06 [1]
##  xtable                               1.8-4     2019-04-21 [1]
##  xts                                  0.11-2    2018-11-05 [1]
##  XVector                              0.22.0    2018-10-30 [1]
##  yaml                                 2.2.0     2018-07-25 [1]
##  zlibbioc                             1.28.0    2018-10-30 [1]
##  zoo                                  1.8-5     2019-03-21 [1]
##  source        
##  CRAN (R 3.5.1)
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.3)
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.2)
##  Bioconductor  
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  local         
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  Bioconductor  
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  Bioconductor  
##  Bioconductor  
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  Bioconductor  
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.1)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.2)
##  CRAN (R 3.5.3)
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.1)
##  Bioconductor  
##  CRAN (R 3.5.3)
## 
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library

Deepak Tanwar

Created on: 2019-04-25
Updated on: 2019-04-30